. Author manuscript; available in PMC: 2018 Feb 17.

Published in final edited form as: Am J Med Genet B Neuropsychiatr Genet. 2015 Dec 11;171B(2):276–289. doi: 10.1002/ajmg.b.32402

TABLE II.

Novel SNPs Demonstrating Specificity to Particular Family History Subgroups

CHR	Mb	SNP (assoc allele)	Info	P_PGC1	Freq_cases		Freq_cont	P_omnibus	Model	Nearest gene (kb)
CHR	Mb	SNP (assoc allele)	Info	P_PGC1	Positive	Negative	Freq_cont	P_omnibus	Model	Nearest gene (kb)
2	40.11	rs7568579 (A)	0.9956	0.036	0.075	0.103	0.11	5.53E-06	+	SLC8A1 (−81.33 kb)
17	10.22	rs3809738 (T)	0.7261	3.45E-04	0.868	0.841	0.854	7.51E-06	−	MYH13 (+0.324 kb) +
9	100.34	rs2779600 (A)	0.9197	2.42E-03	0.565	0.513	0.501	8.28E-06	+	GABBR2 (0)
7	11.6	rs2354954 (A)	0.6895	0.101	0.295	0.323	0.337	1.26E-05	+	THSD7A (0)
16	1.33	rs1132356 (A)	0.8486	0.187	0.132	0.099	0.104	1.30E-05	+	BAIAP3 (0)
9	133.34	rs12552460 (T)	0.9969	7.71E-05	0.851	0.872	0.849	1.70E-05	−	POMT1 (−29.86 kb)
6	150.94	rs9398022 (A)	0.8542	1.27E-03	0.609	0.571	0.559	1.90E-05	+	PLEKHG1 (−23.03 kb)
5	17.06	rs11959796 (A)	0.9155	0.033	0.136	0.161	0.14	2.13E-05	−	MYO10 (+70.02 kb)
11	121.55	rs17126243 (A)	0.9717	1.47E-04	0.058	0.051	0.064	2.54E-05	−	BLID (+62.75 kb)
3	27.57	rs12498098 (T)	0.9933	0.721	0.816	0.854	0.857	2.73E-05	+	SLC4A7 (+100.4 kb) +
12	58.05	rs2203391 (T)	0.981	0.002	0.775	0.802	0.815	2.80E-05	+	SLC16A7 (−314.6 kb)
14	99.69	rs35257667 (A)	0.7317	0.05	0.311	0.278	0.277	2.89E-05	+	DEGS2 (0)
9	89.17	rs1930057 (T)	0.9487	0.002	0.775	0.756	0.779	2.97E-05	−	DAPK1 (−132.9 kb)
19	44.54	rs1375910 (A)	0.7775	0.025	0.064	0.049	0.044	3.00E-05	+	SAMD4B (0)
6	71.8	rs2018220 (A)	0.9694	8.20E-04	0.379	0.4	0.376	3.11E-05	−	B3GAT2 (+78.74 kb) +
14	70.27	rs1476610 (T)	0.988	0.282	0.081	0.11	0.1	3.67E-05	−	MAP3K9 (0)
21	14.38	rs6516605 (C)	0.8042	0.007	0.653	0.614	0.604	3.80E-05	+	LIPI (−24.51 kb)
19	16.6	rs12461484 (C)	0.9134	0.007	0.46	0.424	0.416	3.83E-05	+	MED26 (+4.194 kb) +
5	63.41	rs7737133 (T)	0.7356	0.043	0.008	0.004	0.006	4.01E-05	−	RNF180 (−89.89 kb)
12	127.69	rs12099512 (T)	0.0145	0.801	0.995	0.995	0.995	4.14E-05	+	SLC15A4 (−148.9 kb)
2	96.56	rs11693625 (T)	0.7397	0.01	0.842	0.812	0.801	4.52E-05	+	ARID5A (−9.116 kb)
9	37.89	rs7030885 (A)	0.2433	0.579	0.995	0.998	0.998	4.69E-05	+	MCART1 (0)

For SNPs demonstrating specificity to family history positive or negative schizophrenia, CHR and Mb give its genomic coordinates (hg18); assoc allele represents the tested allele; INFO and P_PGC1 are the imputation information and P-value as reported in the original PGC GWAS; Freq_cases and Freq_cont give the frequency of the tested allele in family history case subgroups and controls;P_omnibus and Model give the significance by 2df omnibus test of “any association” and best-fitting model. For each SNP, the nearest gene within 1 Mb is shown; its position relative to a gene is given parenthetically (negative and positive kb values indicate up- and downstream positions).